dwibiascorrect¶
Synopsis¶
Perform B1 field inhomogeneity correction for a DWI volume series
Usage¶
dwibiascorrect input output [ options ]
- input: The input image series to be corrected
- output: The output corrected image series
Options¶
Options for the dwibiascorrect script¶
- -mask Manually provide a mask image for bias field estimation
- -bias Output the estimated bias field
- -ants Use ANTS N4 to estimate the inhomogeneity field
- -fsl Use FSL FAST to estimate the inhomogeneity field
- -grad Pass the diffusion gradient table in MRtrix format
- -fslgrad bvecs bvals Pass the diffusion gradient table in FSL bvecs/bvals format
Standard options¶
- -continue <TempDir> <LastFile> Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file
- -force Force overwrite of output files if pre-existing
- -help Display help information for the script
- -nocleanup Do not delete temporary files during script, or temporary directory at script completion
- -nthreads number Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)
- -tempdir /path/to/tmp/ Manually specify the path in which to generate the temporary directory
- -quiet Suppress all console output during script execution
- -info Display additional information and progress for every command invoked
- -debug Display additional debugging information over and above the output of -info
References¶
- If using -fast option: Zhang, Y.; Brady, M. & Smith, S. Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. IEEE Transactions on Medical Imaging, 2001, 20, 45-57
- If using -fast option: Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T. E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 2004, 23, S208-S219
- If using -ants option: Tustison, N.; Avants, B.; Cook, P.; Zheng, Y.; Egan, A.; Yushkevich, P. & Gee, J. N4ITK: Improved N3 Bias Correction. IEEE Transactions on Medical Imaging, 2010, 29, 1310-1320
Author: Robert E. Smith (robert.smith@florey.edu.au)
Copyright: Copyright (c) 2008-2017 the MRtrix3 contributors.
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, you can obtain one at http://mozilla.org/MPL/2.0/.
MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see http://www.mrtrix.org/.